rs10135446

Variant names:

• chr14-79943135-G-T
• rs10135446
• ENST00000554307.1:n.366+29167C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554307.1(ENSG00000258416):​n.366+29167C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,968 control chromosomes in the GnomAD database, including 2,512 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2512 hom., cov: 32)
• Consequence: ENSG00000258416 ENST00000554307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

ENSG00000258416 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258416	ENST00000554307.1	n.366+29167C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27130 AN: 151850 Hom.: 2508 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27157 AN: 151968 Hom.: 2512 Cov.: 32 AF XY: 0.183 AC XY: 13616 AN XY: 74248

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.162

Alfa AF: 0.180 Hom.: 2614

Bravo AF: 0.176

Asia WGS AF: 0.157 AC: 544 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10135446; hg19: chr14-80409478;